Swapping the gears is a lot tougher than building a stock 6. You need to take a close look at the shop manual. If you have and know how to use a set of dial indicators you should be able to do it. If not, find someone to help.
Last time I checked some of the vendors carried the 4.10 gears. I would avoid Houser like the plague, he doesn't know much about these trucks.
Randy\'s Ring & Pinion also makes a set of 3.90 gears.